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phyloTop: Calculating Topological Properties of Phylogenies

phyloTop provides tools for calculating and viewing topological properties of phylogenetic trees.

Installing phyloTop

To install the development version from github:

library(devtools)
install_github("michellekendall/phyloTop")

The stable version can be installed from CRAN using:

install.packages("phyloTop")

Then, to load the package, use:

library("phyloTop")

## Loading required package: ape

Content overview

The key functions available in phyloTop are:

Tree statistics and topological properties:

Tree visualisation tools:

Simulating an epidemic and creating the corresponding genealogy:

Examples

Tree statistics:

Apply tree statistic functions to a list of 10 random trees, each with 50 tips:

set.seed(123)
phyloTop(rmtree(10,50))

##    avgLadder cherries colless.phylo ILnumber maxHeight pitchforks sackin.phylo
## 1      0.000       19            82       12         9          9          312
## 2      2.167       16           120       18         9          7          330
## 3      2.500       19           192       12        12          6          394
## 4      2.333       16           139       18        11          9          345
## 5      2.000       18           150       14        10          8          358
## 6      2.333       17           105       16        11         10          321
## 7      2.333       19           112       12        10          5          330
## 8      2.333       15           229       20        13          9          421
## 9      3.000       17           121       16        11          7          331
## 10     3.000       16           181       18        12          7          377
##    stairs1 stairs2
## 1   0.5510  0.7257
## 2   0.5306  0.6752
## 3   0.5102  0.6907
## 4   0.6327  0.6487
## 5   0.5714  0.6880
## 6   0.6122  0.6649
## 7   0.5714  0.6696
## 8   0.6735  0.5760
## 9   0.6122  0.6487
## 10  0.6122  0.6237

Tree visualisation tools:

Plot a random tree with 20 tips, highlighting the the clade(s) descending from nodes 25 and 33:

subtreeShow(rtree(20),nodeList=c(25,33), mainCol="navy", subtreeCol="cyan", nodeLabelCol="cyan", edge.width=2)

Contributing / asking a question

Contributions are welcome via pull requests.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Questions, feature requests and bugs can be reported using the package’s issue system.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.